Sodium in PDB 8uuc: Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G)

The structure of Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G), PDB code: 8uuc was solved by C.H.Trasvina-Arenas, S.S.David, A.J.Fisher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.62 / 1.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	38.832, 84.137, 225.742, 90, 90, 90
R / Rfree (%)	17.6 / 19.7

The structure of Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G) also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G) (pdb code 8uuc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G), PDB code: 8uuc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:37.1 occ:1.00 O A:VAL188 2.7 32.2 1.0 O A:LYS185 2.7 34.3 1.0 O A:HOH519 2.9 37.0 1.0 O A:ALA186 3.5 40.9 1.0 C A:VAL188 3.6 33.0 1.0 C A:LYS185 3.7 32.8 1.0 C A:ALA186 3.8 36.4 1.0 CA A:ALA186 4.2 32.1 1.0 O A:HOH532 4.2 33.2 1.0 N A:VAL188 4.2 32.9 1.0 N A:ASN190 4.3 30.3 1.0 N A:ALA189 4.4 36.3 1.0 N A:VAL187 4.4 34.8 1.0 N A:ALA186 4.4 27.8 1.0 CA A:ALA189 4.4 36.7 1.0 CA A:VAL188 4.5 34.0 1.0 O C:HOH226 4.6 35.6 1.0 O A:LEU184 4.7 30.1 1.0 C A:ALA189 4.7 32.9 1.0 CA A:LYS185 4.7 29.9 1.0 C A:VAL187 4.8 36.6 1.0 CA A:VAL187 5.0 34.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:43.0 occ:1.00 OD2 A:ASP68 2.5 40.0 1.0 O A:HOH571 2.5 48.2 1.0 O A:HOH590 2.6 42.6 1.0 N A:SER65 2.9 35.8 1.0 CG A:ASP68 3.4 36.1 1.0 CA A:ALA64 3.5 32.4 1.0 CB A:ASP68 3.6 31.1 1.0 OG A:SER65 3.6 36.0 1.0 CB A:ALA64 3.6 33.0 1.0 C A:ALA64 3.7 34.1 1.0 CB A:SER65 3.9 33.9 1.0 CA A:SER65 4.0 31.6 1.0 O A:SER65 4.4 30.5 1.0 OD1 A:ASP68 4.5 39.9 1.0 C A:SER65 4.7 29.9 1.0 N A:ALA64 4.8 31.9 1.0 CE1 A:PHE55 4.8 33.5 1.0 O A:HOH428 4.9 36.4 1.0 O A:ALA64 4.9 30.6 1.0

C.H.Trasvina-Arenas, M.Hashemian, M.Malek, S.Merrill, A.J.Fisher, S.S.David. Crystal Structure of Mutyx: A Novel Clusterless Adenine Dna Glycosylase with A Distinct C-Terminal Domain and 8-Oxoguanine Recognition Sphere. Biorxiv 2025.
ISSN: ISSN 2692-8205
PubMed: 39803464
DOI: 10.1101/2025.01.03.631205